High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer

Background

The characterization of copy number alteration patterns in breast cancer requires high-resolution genome-wide profiling of a large panel of tumor specimens. To date, most genome-wide array comparative genomic hybridization studies have used tumor panels of relatively large tumor size and high Nottingham Prognostic Index (NPI) that are not as representative of breast cancer demographics.

Results

We performed an oligo-array-based high-resolution analysis of copy number alterations in 171 primary breast tumors of relatively small size and low NPI, which was therefore more representative of breast cancer demographics. Hierarchical clustering over the common regions of alteration identified a novel subtype of high-grade estrogen receptor (ER)-negative breast cancer, characterized by a low genomic instability index. We were able to validate the existence of this genomic subtype in one external breast cancer cohort. Using matched array expression data we also identified the genomic regions showing the strongest coordinate expression changes ('hotspots'). We show that several of these hotspots are located in the phosphatome, kinome and chromatinome, and harbor members of the 122-breast cancer CAN-list. Furthermore, we identify frequently amplified hotspots on 8q22.3 (EDD1, WDSOF1), 8q24.11-13 (THRAP6, DCC1, SQLE, SPG8) and 11q14.1 (NDUFC2, ALG8, USP35) associated with significantly worse prognosis. Amplification of any of these regions identified 37 samples with significantly worse overall survival (hazard ratio (HR) = 2.3 (1.3-1.4) p = 0.003) and time to distant metastasis (HR = 2.6 (1.4-5.1) p = 0.004) independently of NPI.

Conclusion

We present strong evidence for the existence of a novel subtype of high-grade ER-negative tumors that is characterized by a low genomic instability index. We also provide a genome-wide list of common copy number alteration regions in breast cancer that show strong coordinate aberrant expression, and further identify novel frequently amplified regions that correlate with poor prognosis. Many of the genes associated with these regions represent likely novel oncogenes or tumor suppressors.     

Deregulated expression of Cdc6 in the skin facilitates papilloma formation and affects the hair growth cycle

Cdc6 encodes a key protein for DNA replication, responsible for the recruitment of the MCM helicase to replication origins during the G1 phase of the cell division cycle. The oncogenic potential of deregulated Cdc6 expression has been inferred from cellular studies, but no mouse models have been described to study its effects in mammalian tissues. Here we report the generation of K5-Cdc6, a transgenic mouse strain in which Cdc6 expression is deregulated in tissues with stratified epithelia. Higher levels of CDC6 protein enhanced the loading of MCM complexes to DNA in epidermal keratinocytes, without affecting their proliferation rate or inducing DNA damage. While Cdc6 overexpression did not promote skin tumors, it facilitated the formation of papillomas in cooperation with mutagenic agents such as DMBA. In addition, the elevated levels of CDC6 protein in the skin extended the resting stage of the hair growth cycle, leading to better fur preservation in older mice.     

Benzimidazoles as benzamide replacements within cyclohexane-based CC chemokine receptor 2 (CCR2) antagonists

We describe the design, synthesis, and evaluation of benzimidazoles as benzamide replacements within a series of trisubstituted cyclohexane CCR2 antagonists. 7-Trifluoromethylbenzimidazoles displayed potent binding and functional antagonism of CCR2 while being selective over CCR3. These benzimidazoles were also incorporated into lactam-containing antagonists, thus completely eliminating the customary bis-amide.     

Discovery of an orally-bioavailable CC Chemokine Receptor 2 antagonist derived from an acyclic diaminoalcohol backbone

We describe an isostere-driven approach to improve upon a previously-described series of capped dipeptide antagonists of CC Chemokine Receptor 2 (CCR2). Modification of the substitution around the isostere was combined with additional changes in a distal aromatic substituent to provide single-digit nanomolar antagonists of CCR2. These studies led to the identification of 18, a compound that was suitable for studies in murine models of CCR2 activity.     

Spatiotemporal regulation of Ipl1/Aurora activity by direct Cdk1 phosphorylation

Oscillating cyclin-dependent kinase 1 (Cdk1) activity is the major regulator of cell-cycle progression, whereas the Aurora B kinase, as part of the chromosome passenger complex (CPC), controls critical aspects of mitosis such as chromosome condensation and biorientation on the spindle. How these kinases mechanistically coordinate their important functions is only partially understood. Here, using budding yeast, we identify a regulatory mechanism by which the Cdk1 kinase Cdc28 directly controls the Aurora kinase Ipl1. We show that Cdk1 phosphorylates Ipl1 on two serine residues in the N-terminal domain, thereby suppressing its association with the microtubule plus-end tracking protein Bim1 until the onset of anaphase. Failure to phosphorylate Ipl1 leads to its premature targeting to the metaphase spindle and results in constitutive Bim1 phosphorylation, which is normally restricted to anaphase. Cells expressing an Ipl1-Sli15 complex that cannot be phosphorylated by Cdk1 display a severe growth defect. Our work shows that Ipl1/Aurora is not only the catalytic subunit of the CPC but also an important regulatory target that allows Cdk1 to coordinate chromosome biorientation with spindle morphogenesis.     

Effects of simulated heat waves on an experimental community of pepper plants,green peach aphids and two parasitoid species

Heat waves – extended periods of abnormally hot weather – are predicted to increase in severity and frequency under climate change. The severity of heat waves should impact communities and food webs through effects on performance of individual species and through changes in the strength of interactions between them. This study tested the effects of severity of simulated heat waves, with daily maxima of either 32°C or 40°C, on a tritrophic food web consisting of plants, Capsicum anuum, aphids, Myzus persicae and two parasitoids, Aphidius matricariae and Aphelinus abdominalis. Osmolarity of plant sap (concentration of dissolved solids) was highest under 40°C heat waves, suggesting the presence of secondary plant compounds involved with stress responses. Population growth of aphids was lower under heat waves (both 32°C and 40°C daily maxima), compared to environments with periodic hot days. Development time of parasitoids was longer under heat waves. Heat waves decreased the proportion of winged aphids in the population. When both parasitoid species were present, impacts on aphid populations were greater in heat wave environments than environments with periodic hot days. When either parasitoid species was by itself, heat waves did not affect the interaction between parasitoids and aphids. Numbers of A. matricariae were reduced in heat wave environments, whereas numbers of A. abdominalis were not. In addition to direct effects on individual species, we also obtained indirect evidence for the effects of heat waves on the bottom–up effects of plant stress compounds on herbivore performance, and on the strength of inter and intra‐specific competition. Our results demonstrate that heat waves could have important effects on community structure, and on important, community‐level processes such as intra‐guild interactions and trophic cascades.     

Non-native plants and soil microbes: potential contributors to the consistent reduction in soil aggregate stability caused by the disturbance of North American grasslands

? Soil aggregate stability is an important ecosystem property that is altered by anthropogenic disturbance. Yet, the generalization of these alterations and the identification of the main contributors are limited by the absence of cross-site comparisons and the application of inconsistent methodologies across regions. ? We assessed aggregate stability in paired remnant and post-disturbance grasslands across California, shortgrass and tallgrass prairies, and in manipulative experiments of plant composition and soil microbial inoculation. ? Grasslands recovering from anthropogenic disturbance consistently had lower aggregate stability than remnants. Across all grasslands, non-native plant diversity was significantly associated with reduced soil aggregate stability. A negative effect of non-native plants on aggregate stability was also observed in a mesocosm experiment comparing native and non-native plants from California grasslands. Moreover, an inoculation study demonstrated that the degradation of the microbial community also contributes to the decline in soil aggregate stability in disturbed grasslands. ? Anthropogenic disturbance consistently reduced water-stable aggregates. The stability of aggregates was reduced by non-native plants and the degradation of the native soil microbial community. This latter effect might contribute to the sustained decline in aggregate stability following anthropogenic disturbance. Further exploration is advocated to understand the generality of these potential mechanisms.     

The isoform B of the Dictyostelium long-chain fatty-acyl-coenzyme A synthetase is initially inserted into the ER and subsequently provides peroxisomes with an activity important for efficient phagocytosis

Long-chain fatty-acyl-coenzyme A synthetases activate fatty acids for anabolic or catabolic metabolism. They often localize to more than one organelle within eukaryotic cells. Dictyostelium contains two of these proteins, FcsA and FcsB with the latter being targeted to the membrane of the endoplasmic reticulum by virtue of an N-terminal signal sequence and from there appears to move on to peroxisomes. Deletion of this signal favors the peripheral association of the protein with the mitochondrial surface instead. A strain lacking the activity of the FcsB enzyme was constructed by homologous recombination. It has a severe deficiency in the phagocytic uptake of particles, which can be partially alleviated by a peroxisomally targeted, soluble FcsA enzyme. It is, however, not rescued by expressing FcsA in the cytoplasm or targeting it to the ER, indicating that peroxisomal β-oxidation is important for phagocytosis. In a fcsA(-)/B(-) double mutant phagocytosis efficiency is similar to fcsB(-) cells. However, unlike the single mutants, the fcsA(-)/B(-) strain is delayed in morphogenesis, but forms viable spores, albeit within a small fruiting body. This developmental defect is also seen in other mutants affecting peroxisomal enzymes involved in β-oxidation and the glyoxylate cycle.